scholarly journals The Soil Microbiome Influences Grapevine-Associated Microbiota

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Iratxe Zarraonaindia ◽  
Sarah M. Owens ◽  
Pamela Weisenhorn ◽  
Kristin West ◽  
Jarrad Hampton-Marcell ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Management Practices ◽  
Temporal Dynamics ◽  
Spatial Scales ◽  
C:N Ratio ◽  
Soil Microbiome ◽  
Plant Growth Promoting Bacteria ◽  
Organoleptic Properties ◽  
Associated Bacteria ◽  
Plant Growth Promoting

ABSTRACTGrapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g.,Rhizobiaceaeand Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management.IMPORTANCEVine-associated bacterial communities may play specific roles in the productivity and disease resistance of their host plant. Also, the bacterial communities on grapes have the potential to influence the organoleptic properties of the wine, contributing to a regional terroir. Understanding that factors that influence these bacteria may provide insights into management practices to shape and craft individual wine properties. We show that soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native grapevine microbiome preharvest.

Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Hidehiro Ishizawa ◽  
Masashi Kuroda ◽  
Daisuke Inoue ◽  
Masaaki Morikawa ◽  
Michihiko Ike
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Production Efficiency ◽  
Community Dynamics ◽  
Amplicon Sequencing ◽  
Plant Colonization ◽  
Plant Growth Promoting Bacteria ◽  
Short Period ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACT Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7–32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.

scholarly journals Effects of the Biofertilizer OYK (Bacillus sp.) Inoculation on Endophytic Microbial Community in Sweet Potato

Horticulturae ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 81
Author(s):  
Ahsanul Salehin ◽  
Md Hafizur Rahman Hafiz ◽  
Shohei Hayashi ◽  
Fumihiko Adachi ◽  
Kazuhito Itoh
Keyword(s):  
Plant Growth ◽  
Sweet Potato ◽  
Bacterial Communities ◽  
Ipomoea Batatas ◽  
Diversity Index ◽  
Plant Growth Promoting Bacteria ◽  
Bacillus Sp ◽  
Bacterial Composition ◽  
Plant Growth Promoting ◽  
Growth Promoting

Sweet potato (Ipomoea batatas L.) grows well even in infertile and nitrogen-limited fields, and endophytic bacterial communities have been proposed to be responsible for this ability. Plant-growth-promoting bacteria are considered eco-friendly and are used in agriculture, but their application can interact with endophytic communities in many ways. In this study, a commercial biofertilizer, OYK, consisting of a Bacillus sp., was applied to two cultivars of sweet potato, and the effects on indigenous endophytic bacterial communities in field conditions were examined. A total of 101 bacteria belonging to 25 genera in 9 classes were isolated. Although the inoculated OYK was not detected and significant plant-growth-promoting effects were not observed, the inoculation changed the endophytic bacterial composition, and the changes differed between the cultivars, as follows: Novosphingobium in α-Proteobacteria was dominant; it remained dominant in Beniharuka after the inoculation of OYK, while it disappeared in Beniazuma, with an increase in Sphingomonas and Sphingobium in α-Proteobacteria as well as Chryseobacterium and Acinetobacter in Flavobacteria. The behavior of Bacilli and Actinobacteria also differed between the cultivars. The Shannon diversity index (H) increased after inoculation in all conditions, and the values were similar between the cultivars. Competition of the inoculant with indigenous rhizobacteria and endophytes may determine the fates of the inoculant and the endophytic community.

scholarly journals Dynamics ofPanax ginsengRhizospheric Soil Microbial Community and Their Metabolic Function

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Yong Li ◽  
YiXin Ying ◽  
WanLong Ding
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Restriction Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Plant Growth Promoting Bacteria ◽  
Metabolic Function ◽  
Rhizosphere Soils ◽  
Soil Microbial ◽  
Culture Independent ◽  
Plant Growth Promoting

The bacterial communities of 1- to 6-year ginseng rhizosphere soils were characterized by culture-independent approaches, random amplified polymorphic DNA (RAPD), and amplified ribosomal DNA restriction analysis (ARDRA). Culture-dependent method (Biolog) was used to investigate the metabolic function variance of microbe living in rhizosphere soil. Results showed that significant genetic and metabolic function variance were detected among soils, and, with the increasing of cultivating years, genetic diversity of bacterial communities in ginseng rhizosphere soil tended to be decreased. Also we found thatVerrucomicrobia,Acidobacteria, andProteobacteriawere the dominants in rhizosphere soils, but, with the increasing of cultivating years, plant disease prevention or plant growth promoting bacteria, such asPseudomonas,Burkholderia, andBacillus, tended to be rare.

scholarly journals Spatial synchrony of a threatened shorebird: Regional roles of climate, dispersal and management

2015 ◽  
Vol 26 (1) ◽  
pp. 119-135 ◽  
Author(s):  
LUKE J. EBERHART-PHILLIPS ◽  
BRIAN R. HUDGENS ◽  
MARK A. COLWELL
Keyword(s):  
Management Practices ◽  
Temporal Dynamics ◽  
Spatial Scales ◽  
The United States ◽  
Dispersal Distance ◽  
Species Range ◽  
Spatial Synchrony ◽  
The South ◽  
Threatened And Endangered Species ◽  
Predator Management

SummaryCorrelated climate patterns, dispersal, and similar management practices may synchronise dynamics of populations in close proximity, which tends to reduce metapopulation persistence. However, synchronising and desynchronising mechanisms can act at multiple spatial scales, which means that for wide-ranging species, patterns of spatial synchrony and their causes might vary across the species’ range. We examined the relationships of spatial autocorrelation in winter climate, dispersal distance and predator management to the spatio-temporal dynamics of the Western Snowy Plover Charadrius nivosus nivosus, a threatened shorebird that breeds along the Pacific coast of the United States. We investigated how signals and drivers of plover population growth dynamics vary among populations occupying northern, central, and southern regions of the species’ U.S. range. Across the metapopulation and specifically the core of the species’ range in the south, we found that plover populations within 132 km of each other exhibited detectable levels of synchrony, which fell within published estimates of dispersal distance. Furthermore, similar predator management among sites increased the degree to which nearby populations were synchronised. There was, however, no evidence of spatial synchrony in populations of the northern and central regions. Regional differences in synchrony were associated with different population drivers and structure; prolonged cold periods had the strongest influence on the growth of northern populations while predator management had the strongest influence on southern populations. Northern populations were also smaller than the south, which likely reduced our ability to detect spatial synchrony because of increased demographic stochasticity. Neither climatic nor management variables had a detectable influence on central populations. Although the primary objective of threatened and endangered species management is to increase populations to viable levels, we recommend that conservation biologists and land managers acknowledge region-specific processes when considering the long-term persistence of wide-ranging species and coordinate inter-agency efforts to manage neighbouring populations effectively.

scholarly journals Plant Growth-Promoting Bacteria as Bioinoculants: Attributes and Challenges for Sustainable Crop Improvement

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1167
Author(s):  
Ma. del Carmen Orozco-Mosqueda ◽  
Aurora Flores ◽  
Blanca Rojas-Sánchez ◽  
Carlos A. Urtis-Flores ◽  
Luzmaria R. Morales-Cedeño ◽  
...  
Keyword(s):  
Plant Growth ◽  
Crop Improvement ◽  
Developed Countries ◽  
Plant Growth Promoting Bacteria ◽  
Developing Regions ◽  
Associated Bacteria ◽  
Current State ◽  
Antibiotic Compounds ◽  
Plant Growth Promoting ◽  
Growth Promoting

Plant growth-promoting bacteria (PGPB) are excellent biocontrol agents and stimulators of plant growth, nutrition, and production. Therefore, these plant-associated bacteria are considered an excellent alternative to reduce or eliminate the use of toxic agrochemicals. In this work, we review the current state of the beneficial mechanisms (direct and indirect), including the production of antibiotic compounds and enzymes, facilitation of resource acquisition, or production of stimulating phytohormones/metabolites. Some aspects of the formulation technology and bioinoculant efficiency of diverse PGPBs (e.g., rhizobacteria, phyllobacteria and endophytic bacteria) in the field are also discussed. However, the commercialization and application of these biological agents in agriculture occur mainly in developed countries, limiting their success in developing regions. The possible causes of the delay in the application of bioinoculants for sustainable agriculture and the plausible solutions are also discussed in this study. Finally, the use of PGPBs is currently a priority for sustainable production in agriculture.

scholarly journals The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique

2021 ◽  
Vol 9 (8) ◽  
pp. 1562
Author(s):  
Ivete Sandra Alberto Maquia ◽  
Paula Fareleira ◽  
Isabel Videira e. Castro ◽  
Ricardo Soares ◽  
Denise R. A. Brito ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Fire Regime ◽  
Molecular Taxonomy ◽  
Illumina Miseq ◽  
Plant Growth Promoting Bacteria ◽  
Miombo Woodlands ◽  
Soil Bacterial Diversity ◽  
Pgp Traits ◽  
Plant Growth Promoting ◽  
Ensifer Adhaerens

(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.

scholarly journals The Date Palm Tree Rhizosphere Is a Niche for Plant Growth Promoting Bacteria in the Oasis Ecosystem

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Raoudha Ferjani ◽  
Ramona Marasco ◽  
Eleonora Rolli ◽  
Hanene Cherif ◽  
Ameur Cherif ◽  
...  
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Date Palm ◽  
Arid Ecosystems ◽  
Palm Tree ◽  
Plant Growth Promoting Bacteria ◽  
Pgp Traits ◽  
Environmental Selection ◽  
Plant Growth Promoting ◽  
Growth Promoting

In arid ecosystems environmental factors such as geoclimatic conditions and agricultural practices are of major importance in shaping the diversity and functionality of plant-associated bacterial communities. Assessing the influence of such factors is a key to understand (i) the driving forces determining the shape of root-associated bacterial communities and (ii) the plant growth promoting (PGP) services they provide. Desert oasis environment was chosen as model ecosystem where agriculture is possible by the microclimate determined by the date palm cultivation. The bacterial communities in the soil fractions associated with the root system of date palms cultivated in seven oases in Tunisia were assessed by culture-independent and dependent approaches. According to 16S rRNA gene PCR-DGGE fingerprinting, the shapes of the date palm rhizosphere bacterial communities correlate with geoclimatic features along a north-south aridity transect. Despite the fact that the date palm root bacterial community structure was strongly influenced by macroecological factors, the potential rhizosphere services reflected in the PGP traits of isolates screenedin vitrowere conserved among the different oases. Such services were exerted by the 83% of the screened isolates. The comparable numbers and types of PGP traits indicate their importance in maintaining the plant functional homeostasis despite the different environmental selection pressures.

scholarly journals Effects of Nanoparticles on Plant Growth-Promoting Bacteria in Indian Agricultural Soil

Agronomy ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 140 ◽  
Author(s):  
Sangeeta Chavan ◽  
Vigneshwaran Nadanathangam
Keyword(s):  
Silver Nanoparticles ◽  
Zinc Oxide ◽  
Bacterial Communities ◽  
Zinc Oxide Nanoparticles ◽  
Soil Bacteria ◽  
Engineered Nanoparticles ◽  
Oxide Nanoparticles ◽  
Plant Growth Promoting Bacteria ◽  
Plant Growth Promoting ◽  
Growth Promoting

Soil bacteria are some of the key players affecting plant productivity. Soil today is exposed to emerging contaminants like metal engineered nanoparticles. The objective of this study was to evaluate the toxicological effects of silver and zinc oxide nanoparticles on bacteria classified as plant growth-promoting bacteria. Three types of bacteria—nitrogen fixers, phosphate solubilizers, and biofilm formers—were exposed to engineered nanoparticles. Initially, the effect of silver and zinc oxide nanoparticles was determined on pure cultures of the bacteria. These nanoparticles were then applied to soil to assess changes in composition of bacterial communities. Impacts of the nanoparticles were analyzed using Illumina MiSeq sequencing of 16S rRNA genes. In the soil used, relative abundances of the dominant and agriculturally significant phyla, namely, Proteobacteria, Actinobacteria, and Firmicutes, were altered in the presence of silver nanoparticles. Silver nanoparticles changed the abundance of the three phyla by 25 to 45%. Zinc oxide nanoparticles showed negligible effects at the phylum level. Thus, silver nanoparticles may impact bacterial communities in soil, and this in turn may influence processes carried out by soil bacteria.

scholarly journals Priming Effects of Cover Cropping on Bacterial Community in a Tea Plantation

2021 ◽  
Vol 13 (8) ◽  
pp. 4345
Author(s):  
Fo-Ting Shen ◽  
Shih-Han Lin
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Management Practices ◽  
Amplicon Sequencing ◽  
Community Diversity ◽  
Plant Growth Promoting Bacteria ◽  
Metabolic Potential ◽  
Tea Plantation ◽  
Cover Cropping ◽  
Tea Plantations

The acidic nature of red soil commonly found in tea plantations provides unique niches for bacterial growth. These bacteria as well as soil properties are dynamic and vary with agricultural management practices. However, less is known about the influence of manipulation such as cover cropping on bacterial communities in tea plantations. In this study a field trial was conducted to address the short-term effects of soybean intercropping on a bacterial community. Diversity, metabolic potential and structure of the bacterial community were determined through community level physiological profiling and amplicon sequencing approaches. Cover cropping was observed to increase soil EC, available P, K, and microelements Fe, Mn, Cu, and Zn after three months of cultivation. Bacterial functional diversity and metabolic potential toward six carbon source categories also increased in response to cover cropping. Distinct bacterial communities among treatments were revealed, and the most effective biomarkers, such as Acidobacteriaceae, Burkholderiaceae, Rhodanobacteraceae, and Sphingomonadaceae, were identified in cover cropping. Members belonging to these families are considered as organic matter decomposers and/or plant growth promoting bacteria. We provided the first evidence that cover cropping boosted both copiotrophs (Proteobacteria) and oligotrophs (Acidobacteria), with potentially increased functional stability, facilitated nutrient cycling, and prospective benefits to plants in the tea plantation.

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